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What is FASTA format?

FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length.

An example sequence in FASTA format is:

>gi|186681228|ref|YP_001864424.1| phycoerythrobilin:ferredoxin oxidoreductase
MNSERSDVTLYQPFLDYAIAYMRSRLDLEPYPIPTGFESNSAVVGKGKNQEEVVTTSYAFQTAKLRQIRA
AHVQGGNSLQVLNFVIFPHLNYDLPFFGADLVTLPGGHLIALDMQPLFRDDSAYQAKYTEPILPIFHAHQ
QHLSWGGDFPEEAQPFFSPAFLWTRPQETAVVETQVFAAFKDYLKAYLDFVEQAEAVTDSQNLVAIKQAQ
LRYLRYRAEKDPARGMFKRFYGAEWTEEYIHGFLFDLERKLTVVK

Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions:

• lower-case letters are accepted and are mapped into upper-case;
• a single hyphen or dash can be used to represent a gap of indeterminate length;
• in amino acid sequences, U and * are acceptable letters (see below).
• any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).

The nucleic acid codes are:

        A --> adenosine           M --> A C (amino)
        C --> cytidine            S --> G C (strong)
        G --> guanine             W --> A T (weak)
        T --> thymidine           B --> G T C
        U --> uridine             D --> G A T
        R --> G A (purine)        H --> A C T
        Y --> T C (pyrimidine)    V --> G C A
        K --> G T (keto)          N --> A G C T (any)
                                  -  gap of indeterminate length

The accepted amino acid codes are:

    A ALA alanine                         P PRO proline
    B ASX aspartate or asparagine         Q GLN glutamine
    C CYS cystine                         R ARG arginine
    D ASP aspartate                       S SER serine
    E GLU glutamate                       T THR threonine
    F PHE phenylalanine                   U     selenocysteine
    G GLY glycine                         V VAL valine
    H HIS histidine                       W TRP tryptophan
    I ILE isoleucine                      Y TYR tyrosine
    K LYS lysine                          Z GLX glutamate or glutamine
    L LEU leucine                         X     any
    M MET methionine                      *     translation stop
    N ASN asparagine                      -     gap of indeterminate length